Human and murine neutrophils share core transcriptional programs in both homeostatic and inflamed contexts
This repository contains the code accompanying the manuscript "Human and murine neutrophils share core transcriptional programs in both homeostatic and inflamed contexts". Raw data to reproduce analyses in this repository can be obtained as detailed in the reporting summary.
Below is a table summarizing important software requirements that are needed to generate the analyses and figures discussed in our manuscript. All analyses except for alignment of raw fastq files were run on an M1 MacBook Pro (13-inch, M1, 2020; MacOS 12.5.1). Our code has been run and tested on the aforementioned infrastructure, no non-standard hardware is required to execute the code.
| Software | Version |
|---|---|
| R | 4.2.0 |
| Bioconductor | 3.15 |
| magick | 2.7.3 |
| DESeq2 | 1.36.0 |
| ggvenn | 0.1.9 |
| circlize | 0.4.15 |
| ggsci | 2.9 |
| RColorBrewer | 1.1-3 |
| viridis | 0.6.2 |
| viridisLite | 0.4.0 |
| MASS | 7.3-57 |
| rstatix | 0.7.0 |
| ggbreak | 0.0.9 |
| reshape2 | 1.1.4 |
| kSamples | 1.2-9 |
| SuppDists | 1.1-9.7 |
| gridExtra | 2.3 |
| ggrastr | 1.0.1 |
| ggtext | 0.1.1 |
| EnhancedVolcano | 1.14.0 |
| ComplexHeatmap | 2.12.0 |
| ggrepel | 0.9.1 |
| ggpubr | 0.4.0 |
| edgeR | 3.38.1 |
| limma | 3.52.1 |
| SummarizedExperiment | 1.26.1 |
| Biobase | 2.56.0 |
| GenomicRanges | 1.48.0 |
| GenomeInfoDb | 1.32.2 |
| IRanges | 2.30.0 |
| S4Vectors | 0.34.0 |
| BiocGenerics | 0.42.0 |
| MatrixGenerics | 1.8.0 |
| matrixStats | 0.62.0 |
| biomaRt | 2.52.0 |
| BiocManager | 1.30.18 |
| zeallot | 0.1.0 |
| magrittr | 2.0.3 |
| forcats | 0.5.1 |
| stringr | 1.4.0 |
| dplyr | 1.0.9 |
| purrr | 0.3.4 |
| readr | 2.1.2 |
| tidyr | 1.2.0 |
| tibble | 3.1.7 |
| ggplot2 | 3.3.5 |
| tidyverse | 1.3.1 |
| org.Hs.eg.db | 3.15.0 |
| TxDb.Hsapiens.UCSC.hg38.knownGene | 3.15.0 |
| GenomicFeatures | 1.48.3 |
| AnnotationDbi | 1.58.0 |
| goseq | 1.48.0 |
| geneLenDataBase | 1.32.0 |
| BiasedUrn | 1.07 |
| vsn | 3.64.0 |
| survcomp | 1.46.0 |
| prodlim | 2019.11.13 |
| Matrix | 1.4-1 |
| qvalue | 2.28.0 |
| apeglm | 1.18.0 |
| qusage | 2.30.0 |
| fgsea | 1.22.0 |
| msigdbr | 7.5.1 |
| sva | 3.44.0 |
| BiocParallel | 1.30.2 |
| genefilter | 1.78.0 |
| mgcv | 1.8-40 |
| nlme | 3.1-157 |
| GEOquery | 2.64.2 |
| rhdf5 | 2.40.0 |
| jsonlite | 1.8.0 |
| httr | 1.4.3 |
| readxl | 1.4.0 |
| gridtext | 0.1.4 |
| writexl | 1.4.0 |
| cowplot | 1.1.1 |
| lme4 | 1.1-29 |
| DoRothEA | 1.8.0 |
| decoupleR | 2.2.2 |
| CATLYST | 1.16.2 |
| matplotlib | 3.5.1 |
| python | 3.9.1 |
| HOMER | v4.11 |
| marge | v0.0.4.9999 |
| RVAideMemoire | 0.9-81-2 |
Clone this repository ,e.g., by running git clone https://github.com/rgb-lab/inflamed_neutrophil_transcriptome.git. Running this command will take below one minute on most current hardware and internet connections.
To start reproducing the analyses, replace the data/raw_data/ folder with the raw data folder that can be downloaded from a separate repository (please refer to reporting summary). After replacing that folder, you can start executing the included scripts.
All relevant scripts to generate results and figures discussed in the manuscript can be found in the scripts/ folder. The suggested order to run the steps of the analysis is as following. Within each folder, .Rmd files are numbered according to the suggested/required run order.
scripts/haemopedia/*scripts/inflammatory_meta/*scripts/zymosan/*scripts/experimental_validation/*generate_figures.R(depends on the data generated by aforementioned steps)
A majority of the analyses can be run within 1–2 hours on hardware similar to ours.
.
├── data # Contains all data needed for the analysis.
│ ├── metadata # metadata, part of this repo
│ ├── processed # generated, content not part of vcs
│ └── raw_data # downloaded, content not part of vcs
├── figures # Container for generated figures.
├── scripts # Contains all scripts and utils required.
│ ├── experimental_validation # code relating to the validation experiments
│ ├── generate_figures.R # the script that can be run to generate the manuscript's figures
│ ├── haemopedia # code pertaining the haemopedia analysis
│ ├── inflammatory_meta # code to analyze the inflammatory dataset
│ ├── utils # various utils for data retrieval, plotting, ...
│ └── zymosan # zymosan analysis scripts
├── README.md
├── inflammatory_metaanlysis.Rproj
└── .gitignore
Summary diagram of the figure generation mechanism.
flowchart TD
g1[Rmd files] -. calls build function .-> g2{figure_builder.R}
g2 -- returns plot object --> g1
g3[generate_figures.R] -. calls build function .-> g2
g2 -- returns plot object --> g3
g3 -- arranges subfigures --> g5(final PDF figure file)
g4[config.R] -- provides palettes/... --> g2
g1 -- generate --> g6[(Result data files)]
g6 -- loaded by --> g2